REF: Refactoring of the EEG pipeline and stages before integration in the BIDS App

[sebastientourbier]

This PR consists of a big refactoring of the code for the EEG pipeline, stages, and interfaces to:

• make sure data is completely abstracted in the interfaces and the parameter can be set from the stage config
• handle dataset that have sessions
• allow to save the EEG pipeline configuration file
• add a new stage to compute the connectome

All these changes were necessary before integrating the EEG pipeline in the BIDS App.

[codecov[bot]]

Codecov Report

Merging #198 (9f4057a) into release/v3.1.0 (ccbd0ea) will decrease coverage by 0.52%. The diff coverage is 49.45%.

@@                Coverage Diff                 @@
##           release/v3.1.0     #198      +/-   ##
==================================================
- Coverage           72.66%   72.14%   -0.53%     
==================================================
  Files                  35       36       +1     
  Lines                7822     7963     +141     
==================================================
+ Hits                 5684     5745      +61     
- Misses               2138     2218      +80     

Impacted Files	Coverage Δ
cmp/pipelines/functional/fMRI.py	74.34% <ø> (ø)
cmtklib/util.py	58.33% <10.00%> (-6.54%)	:arrow_down:
cmp/project.py	61.81% <16.66%> (-0.22%)	:arrow_down:
cmtklib/config.py	67.75% <40.00%> (-2.68%)	:arrow_down:
cmp/stages/connectome/eeg_connectome.py	50.00% <50.00%> (ø)
cmtklib/bids/io.py	76.70% <58.33%> (-22.30%)	:arrow_down:
cmtklib/connectome.py	91.23% <66.66%> (ø)
cmp/pipelines/anatomical/anatomical.py	79.15% <100.00%> (ø)
cmp/stages/connectome/connectome.py	100.00% <100.00%> (ø)
cmp/stages/connectome/fmri_connectome.py	100.00% <100.00%> (ø)
... and 2 more

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[sebastientourbier]

Dear all, I went further on the integration of the EEG pipeline into the BIDS App and the GUI. Seems thing are working, so I will merge each of the corresponding individual PR branch into the v3.1.0 release, and then I will ask your review from here, that would be simpler.